This is an internal error that gets thrown extracting a cuffdiff step that you had in that particular history. The problem is that values weren't found for the conditions or replicates due to it being an old version of the tool wrapper, 0.0.5, which is no longer available on the server. Basically, the available tool wrapper versions expect parameters the version at the time you ran this did not have, so Galaxy doesn't know how to map parameters to your tool in the workflow it's trying to create.

This should definitely be handled a little better by the extract code, but since that's going to be a code fix on our end you may want to re-try extract and leave the cuffdiff step unchecked. You can edit the newly extracted workflow at that point and add it back in.

You could also re-run the cuffdiff step (with the newer version of the tool -- you'll see what I mean), and then re-extract but make sure to check the *new* cuffdiff step and *not* the old one.

Yes! The problem is caused by the tool version difference between now and previously, which is also warning behind each tool, like: Dataset was created with tool version "0.0.5", but workflow extraction will use version "0.0.6".